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1. Field of the Invention
The present invention relates to systems, methods, and products for making and scanning arrays of biological materials.
2. Related Art
Synthesized probe arrays, such as Affymetrix(copyright) GeneChip(copyright) arrays, have been used to generate unprecedented amounts of information about biological systems. For example, a commercially available GeneChip(copyright) array set from Affymetrix, Inc. of Santa Clara, Calif., is capable of monitoring the expression levels of approximately 6,500 murine genes and expressed sequence tags (EST""s). Experimenters can quickly design follow-on experiments with respect to genes, EST""s, or other biological materials of interest by, for example, producing in their own laboratories microscope slides containing dense arrays of probes using the Affymetrix(copyright) 417(trademark) Arrayer or other spotting devices.
Analysis of data from experiments with synthesized and/or spotted probe arrays may lead to the development of new drugs and new diagnostic tools. In some conventional applications, this analysis begins with the capture of fluorescent signals indicating hybridization of labeled target samples with probes on synthesized or spotted probe arrays. The devices used to capture these signals often are referred to as scanners, an example of which is the Affymetrix(copyright) 428(trademark) Scanner from Affymetrix, Inc. of Santa Clara, Calif.
There is a great demand in the art for methods for organizing, accessing and analyzing the vast amount of information collected by scanning microarrays. Computer-based systems and methods have been developed to assist a user to obtain and visualize the vast amounts of information generated by the scanners. These commercial and academic software applications typically provide such information as intensities of hybridization reactions or comparisons of hybridization reactions. This information may be displayed to a user in graphical form.
In accordance with some embodiments of the present invention, a computer program product is described that includes an arrayer manager application and a scanner control application. The arrayer manager application receives and stores location data corresponding to a plurality of probe-feature locations on a substrate. The scanner control application accesses the location data and causes scanning of the substrate based, at least in part, on the accessed location data.
In some implementations, the arrayer manager application and the scanner control application may be separate computer programs, and they may be executed on separate computers. For example, the arrayer manager application may be executed on a first computer that controls an arrayer, and the scanner control application may be executed on a second computer that controls a scanner.
One advantage provided by the computer program product, whether executed on separate computers or a same computer, is that a user wishing to scan a probe array need not provide information regarding the locations of probes on the array""s substrate. Rather, the scanner user simply specifies or selects a file or other data storage structure in which the location data has been stored. The user need not be the same user that caused the location data to be stored by specifying probe-feature locations on the substrate. Thus, for example, the scanner user need not be familiar with, or have knowledge of, the scheme for arraying probes on the substrate as determined by the arrayer user. One scanner user may scan arrays prepared by numerous array users. More generally, the arraying and scanning operations may occur at separate places and times as well as involve separate personnel. This flexibility generally simplifies the scanning operation and reduces the possibilities of error in determining appropriate scanning areas on substrates.
In one embodiment, a computer program product is described that includes a user-interface manager. The user interface manager enables user specification of a plurality of probe-feature locations on a substrate, and provides location data corresponding to the probe-feature locations. The computer program product also includes a data storage manager that stores the location data in a memory unit. Yet another element of the product is an output manager enabled to provide the location data to a scanner control application. This scanner control application causes scanning of the substrate based, at least in part, on the accessed location data. The user interface manager may enable user specification of the probe-feature locations by specifying one or more spacing distances between probe features, by specifying one or more patterns of probe feature locations, and/or by specifying coordinates. The coordinates may include x and y coordinates.
In other embodiments, a computer program product is described that includes a data retriever that accesses location data corresponding to a plurality of probe-feature locations on a substrate. The product also has a scan-area controller that controls scanning of the substrate based, at least in part, on the accessed location data. This location data is stored in a memory unit of a first computer that, in some implementations, controls an arrayer. The data retriever may provide a user interface that enables user selection of the location data, and may access the location data based, at least in part, on the user selection. The data retriever may receive the location data from the first computer and store the location data in a memory unit of a second computer, which may control a scanner. In Some implementations, the probe-feature locations include locations of probes of a spotted array, or of a synthesized array.
In further embodiments, a method is described that includes (a) receiving location data corresponding to a plurality of probe-feature locations on a substrate; (b) storing the location data; (c) accessing the location data; and (d) scanning the substrate based, at least in part, on the accessed location data. Step (a) may include providing a first user interface that enables user specification of the probe feature locations. Step (c) may include (i) providing a second user interface that enables user selection of the location data; and (ii) accessing the location data based, at least in part, on the user selection. In some implementations, step (b) includes storing the location data in an array content file in a memory unit of a first computer, which may control an arrayer. Step (c) in these implementations may include (i) transferring the location data from the first computer to a memory unit of a second computer; (ii) providing a second user interface that enables user selection of the location data; and (iii) accessing the location data from the memory unit of the second computer based, at least in part, on the user selection. The second computer may control a scanner.
Another described embodiment is a method including (a) accessing location data corresponding to a plurality of probe-feature locations on a substrate, wherein the location data is stored in a memory unit of a computer; and (b) scanning the substrate based, at least in part, on the accessed location data.
A further embodiment is a scanning system that includes a scanner and a computer program product. The product has a data retriever that accesses location data corresponding to a plurality of probe-feature locations on a substrate, and a scan-area controller that controls scanning by the scanner of the substrate based, at least in part, on the accessed location data.
Yet a further embodiment is a scanning system having a computer, a scanner, and a computer program product. The product, when executed on the computer, performs a method including accessing location data corresponding to a plurality of probe-feature locations on a substrate, and controlling scanning by the scanner of the substrate based, at least in part, on the accessed location data.
The above embodiments and implementations are not necessarily inclusive or exclusive of each other and may be combined in any manner that is non-conflicting and otherwise possible, whether they be presented in association with a same, or a different, aspect of the invention. The description of one embodiment or implementation is not intended to be limiting with respect to other embodiments or implementations. Also, any one or more function, step, operation, or technique described elsewhere in this specification may, in alternative embodiments or implementations, be combined with any one or more function, step, operation, or technique described in the summary. Thus, the above embodiments and implementations are illustrative rather than limiting.